drug-discovery

Query ChEMBL, PubChem, OpenFDA, and OpenTargets for compound bioactivity, drug-likeness, and interaction data.

Updated Aug 22, 2026
One-click install
npx skills add https://github.com/vivekgoquest/hermes-agent-stable --skill drug-discovery-vivekgoquest
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: drug-discovery
Source: https://github.com/vivekgoquest/hermes-agent-stable/tree/main/optional-skills/research/drug-discovery
Command: npx skills add https://github.com/vivekgoquest/hermes-agent-stable --skill drug-discovery-vivekgoquest

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve? Pharmaceutical research requires pulling compound, bioactivity, and safety data from multiple public databases, each with its own API and query syntax. This Skill consolidates ChEMBL, PubChem, OpenFDA, and OpenTargets lookups into ready-to-run commands and scripts so researchers can screen molecules and targets without writing API boilerplate. ## Core Features & Use Cases - Bioactive Compound Search: Find targets and their active compounds in ChEMBL by name or ChEMBL ID, filtered by pChEMBL potency thresholds. - Drug-Likeness Screening: Evaluate molecules against Lipinski's Rule of Five and Veber's oral bioavailability rules using PubChem property data, including batch screening via the ro5_screen.py script. - Safety & Interaction Lookup: Retrieve drug interaction text from FDA labels and top reported adverse events from OpenFDA, plus gene-disease associations from OpenTargets. - Use Case: A medicinal chemist evaluating a lead series can batch-screen candidate compounds for Ro5 compliance, check the top hit's adverse event profile, and pull known bioactivities against the intended target in one session. ## Quick Start Ask the agent to check whether aspirin passes Lipinski's Rule of Five and look up its known drug interactions.

Frequently Asked Questions about drug-discovery

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search ChEMBL for compounds active against a target?▼

Query the ChEMBL target search endpoint with a target name like EGFR to get its ChEMBL ID, then request activities filtered by pchembl_value__gte for potency. The included chembl_target.py script automates both steps and lists unique molecules ranked by pChEMBL.

How to check if a compound passes Lipinski's Rule of Five?▼

Fetch MolecularWeight, XLogP, HBondDonorCount, and HBondAcceptorCount from the PubChem PUG REST API and compare against the Ro5 thresholds. The ro5_screen.py script batch-screens multiple compound names and reports violations plus Veber rule results.

Do these drug discovery APIs require an API key?▼

No. ChEMBL, PubChem, OpenFDA, and OpenTargets are free public APIs requiring no authentication. ChEMBL has rate limits, so add a short sleep between batch requests to avoid throttling.

Can I screen multiple compounds for drug-likeness at once?▼

Yes. Pass compound names as arguments or via stdin to ro5_screen.py, which fetches PubChem properties for each and prints a pass/fail summary against both Lipinski Ro5 and Veber rules with a 0.3 second delay between requests.

What are the limitations of OpenFDA adverse event data?▼

OpenFDA event data reflects voluntarily reported adverse events, which do not establish causation and may be incomplete or duplicated. It is useful for signal detection but clinical decisions should always involve a licensed pharmacist or physician.